Ten's Misfortune
by ZeeIsTrans
Summary: Gwen notices the TARDIS' pattern in rift reports, and helps Jack locate the Doctor. But what they find, is not how they last saw him. WARNING(S): Mentions of rape, depictions of torture Ships: Definite Jack/Ten mentions
1. Chapter 1

Two Years Ago

The man threw a knife at the Doctor. Luckily, he dodged it. Even though he was chained to a railing, he had enough room to dodge any projectiles thrown by his captor. "Stop avoiding your punishments!" The man yelled, slamming the remaining knives down next to the Doctor. He punched the Doctor with all the force he could manage. The Doctor already had a broken nose, and now he was sure his jaw was almost shattered. "Why don't you just kill me, it's obvious that's your intent?" The Doctor winced at the pain of speaking.

"Why, it wouldn't be as much fun, Time Lord." The man offered.

"How do you know that?"

The man tapped his temple with his index finger, and said, "Telepathic."

"My name is Jet, by the way." The man added.

With that, he kicked the Doctor in the chest, causing him to lose consciousness from the pain.

Torchwood Hub, Cardiff, South Wales, 2009

Jack and Ianto sat on the couch in Jack's office, drinking coffee (specially made by Ianto). Gwen came rushing in, carrying a pile of rift reports.

"Jack!" She panted.

Jack set the coffee down on an end table, and looked at the rift report on top of the pile.

"That's...That's the pattern we've seen every time the Doctor arrives." He grabbed the pile, and flipped through the papers.

"He hasn't left, and he arrived over two years ago!" Jack exclaimed.

"Trace where the TARDIS is, and hopefully we'll find him." He ordered Gwen.

Ianto walked with Jack to the Car once Gwen figured out the location, using Tosh's old computer. They drove until they were on the outskirts of Cardiff, and saw the TARDIS. Jack and Ianto ran over to it, and Jack opened it with his key. What they saw almost toor Jack's heart in half.

The Doctor was chained to one of the TARDIS' railings, naked and covered in blood.

"Oh, shit!" Jack yelled. He ran over to the Doctor and checked his pulses. They were there, but weak.

"Ianto, I need you to help me carry him to the SUV!"

Ianto nodded and they got him into the car with no trouble due to his unfortunate lack of consciousness. The ride back to the hub was a depressing and silent time. Neither Jack or Ianto spoke after getting the Doctor into the SUV.

Gwen helped them get the Doctor into the medbay.

"H-how did this happen, Jack?" Gwen asked, leaning on the medbay railing with her immortal friend.

"I've no idea, but whoever did this is gonna pay." Jack clenched his fists.

Their conversation was broken by a piercing scream from the Doctor. Jack rushed down the stairs to the Doctor's side, Gwen following after him.

"Jack.." The Doctor rasped out, and screamed again.

"Doctor, calm down, it's okay. You're safe." Jack reassured. The Doctor's breathing evened out, and he calmed down. He slowly fluttered his eyes open.

"Hey, Doc." Jack said, putting his hand on his shoulder. The Time Lord flinched away, holding his shoulder protectively.

"He...used to do that." The Doctor said, just loud enough for Jack to hear it.

"Do you want some water?" Gwen asked, still shocked by the whole situation. She hadn't ever met the Doctor in person. On the subwave, she only ever learned how he looked. As she said on the Subwave, he didn't have the appearance she imagined. After talking to him, she was genuinely interested in learning more about him. But due to Torchwood and its terrible timing, she never got a chance to explore the mysteries surrounding the wonderful Time Lord.

The Doctor nodded, and Gwen left the room to get him water.

"What happened? You don't have to answer if you're not ready yet." Jack asked, being cautious not to seem forceful.

The expression on the Doctor's face hardened.

"I...I don't want to talk about it now, Jack." His voice broke, but he concealed the urge to sob.

"Alright. I'm going to go spend some time with Ianto. Gwen will be in in a little bit. You going to be okay alone?" Jack checked. The Doctor nodded, and after Jack left, Gwen entered the room.

"Hey sweetheart, how're you feeling?" Gwen asked, setting the water on the trolley they used as a nightstand for him. The Doctor simply groaned, and hastily drank the water.

Gwen sighed, and sat on a stool next to the Doctor. Again, she was wondering how this was her way of acquainting with the Doctor. Jack filled her in on how heroic and strong the Doctor was, but seeing him like this made her doubt him. Her thoughts were broken by the Doctor stirring. She hopped off the stool, and made sure he was okay.

"Gwenyth…" The Time Lord whispered, his eyes still closed.

Gwen ignored the fact that he called her by the wrong name, and shushed him, soothingly.

"It's alright, love. You'll be alright."

The Doctor seemed to calm down, and ended up drifting to sleep. Gwen went out of the medbay, and called Jack.

"How is he?" Jack asked, not bothering with a proper greeting.

Gwen winced at the intensity in his voice, but understood and replied.

"I got him to drink some water, and now he's asleep." She reassured. Gwen heard Jack sigh over the phone.

"I'll be back in a bit." Jack said, and hung up.

"Ianto, let's go!" Jack called over to him.

Ianto walked out of the kitchen in his flat, and met Jack by the front door. They drove to the hub, Ianto slightly pouting that they weren't able to spend more time together. After all, he didn't really like the Doctor very much, so he couldn't care less if he was in trouble. Gwen met them as they entered the hub, and followed them to the medbay. The Doctor was still sleeping soundly.

"I should call Martha. We still need to fix him up." Jack suggested.

Ianto and Gwen silently agreed, too shocked by the surreal atmosphere in the hub, currently. Jack left the room to call Martha, leaving only Gwen and Ianto with the Doctor.


	2. Chapter 2

"Hello?"

"I need you to come to the hub, _now_."

"What's happened?"

"Just...Just get over here." He ended the call.

When Martha got to the hub, the atmosphere was almost chilling. Jack greeted her at the door as normal, and led her to the medbay. The Doctor was still asleep, but not peacefully. Jack shook the Doctor awake, gently.

"NO!" He screamed and began to writhe on the table.

Martha and Jack both tried to calm him by telling him soothing words and at the same time, holding him still. Their attempts were a failure, the Doctor didn't calm down.

"Martha, get the all-species sedative!" Jack ordered, still trying to hold the Doctor down, but to no avail. Martha did as she was told, and injected the sedative into the top of the Doctor's arm. Almost immediately, he went limp.

"We should check his vitals." Jack suggested, urgently.

Martha nodded and hooked the Doctor up to a heart monitor. Both were flatlined. Jack ran for the defibrillation unit, and stuck the defibrillation pads on both sides of the Doctor's chest. Martha activated it, but there was no response. She tried again on a higher setting, and one of his hearts were active. Jack sighed with relief when Martha got both hearts going. The Doctor writhed and seized, falling off the table, Jack failing to catch him. "Doc, come on, wake up." Jack almost begged, on the verge of tears. As if the Doctor heard him, he opened his eyes.

"Hey." The Doctor replied.

Jack smiled a big grin. He was so relieved the Doctor wasn't gone. If he was, he didn't know what he would do with himself. The Universe would be in extreme danger without the Doctor, every stupid ape on earth and elsewhere would probably not be alive. In fact, every species in this Universe would be in danger.

"How're you feeling?" Jack asked, eager to care for this man, this man he loved indefinitely.

The Doctor grunted in response. It felt like he had been pummeled and trampled on by various alien animals that he couldn't think of the names of due to his excruciating pain in his right leg and everywhere else. The Doctor's eyes closed and he fainted. Jack sighed. This was going to take a while. Jack eased the Doctor back onto the medbay table, and covered him with a duvet.

He walked up the stairs and met Gwen in the main area of the hub.

"Is he doing better at all?" She asked. Jack simply shook his head and went up to his office.

Shortly after, Martha came up to the main area of the hub as well.

"He's got a fractured femur." Martha advised Gwen.

"That's not too bad, I suppose." Gwen tried to make light of the situation. Although, when she thought about it, there wasn't much good at all about what happened.

"But he's not human, Gwen. You've got to remember that. He often talked about how a broken femur or any injury on his femur for a Time Lord is a bloody nightmare." Martha reminded her. Their conversation was interrupted by a scream from the medbay.

Martha rushed down the stairs and shushed the Doctor, trying to calm him but, was not successful.

"WHERE AM I?!" The Doctor demanded. He was panting, and his heart monitor showed both his hearts were racing.

"Doctor, you're in Torchwood Three, remember?" Martha checked.

The Doctor seemed to go limp, but then rolled over, asleep. Jack ran down to the Doctor's side as soon as Martha called for him.

"What happened? Is he okay?" He was panicked. What kind of monster would do this to the man responsible for all these worlds still safe? Who would look at the Doctor and think he deserved all that had been done to him? These questions were nowhere close to being answered by probably anyone.

"He's got multiple broken bones and fractures. The one I'm most concerned about is his femur. When I travelled with him, he mentioned that if he hurt his femur at all, he would be in horrendous pain." Martha advised Jack, sighing.

"Damn. But I heard him scream, what was wrong?" Jack needed to know why he would scream like that. It was terrible. He was crouched next to the Doctor's 'bed', stroking his head subconsciously.

"He didn't know where he was. Jack, I've only ever seen him in that much pain once before. I never wanted to hear something like that scream again." Martha sighed.

Jack felt so much pity for Martha. She had told him she fancied the Doctor while they were travelling, and to see someone you love in pain is equally painful. Jack knew this now. The impossible Time Lord that he loved was in pain. He wanted the Doctor never to be in pain or be upset, but it seemed the Universe had other ideas.

"I'm sorry, Martha." Was all he could say. Martha showed a small smile, but it didn't last very long. Jack didn't expect it to.

Jack heard the Doctor groan in his sleep, and immediately went to his side to stroke his head, soothingly. The Doctor's eyes opened, and he looked up at Jack.

"Hey." Jack greeted, smiling.

"My leg…" The Doctor said, and groaned deeply.

Martha walked closer to his 'bed'. She moved the duvet so that the Doctor could see what happened and why he was hurting so bad. He grimaced at the state of his leg, then realized what was wrong. His femur must have been injured by... _Him_. Oh, god. _Him_. That evil monster that tortured him in his own damn TARDIS. He disabled the TARDIS' defense mechanism, so she couldn't fight him. He had been raped, tortured, and experimented on by that fucking _monster_.

"I reset it and put a cast on it, so it should heal faster, now." Martha advised, breaking him away from his thoughts.

All the Doctor did was nod. He was most definitely not in the mood to talk at all. His leg felt like it had been smashed in with a variety of hammers. He was in so much pain, and felt like he needed to cry. Jack saw a tear slip down the Doctor's cheek, and it broke his heart. Again, the question went through his mind; what monster could have done this to the amazing Time Lord? One thing was for sure, when he found out, there would be bloody Hell to pay.

"What's wrong, Love?" Martha asked, noticing the multiple tears now streaming down the Doctor's cheeks.

When he tried to answer, all that came out was the worst sound both Martha and Jack had ever heard. It was a cross between a sob and a scream. This time, it broke both of their hearts.

"Oh, sweetheart, please tell me what's wrong. Is it your leg?" Martha asked, helplessly. He nodded and groaned.

Martha added to the drip a higher dose of Time Lord-modified-Morphine. The Doctor seemed to relax, and both Jack and martha breathed a sigh of relief that his pain had lessened.


	3. Chapter 3

Jack stayed with the Doctor while Martha went home to get some much needed sleep after a stressful day. He was stroking the Doctor's head as he'd done before whenever the Doctor slept. Whenever he began to stir, Jack shushed him and made sure he stayed asleep.

As he was walking out of the medbay to get a cup of coffee for himself and a cup of tea for the Doctor when he woke up, the door to the Hub rolled open. It was an extremely angry-looking man with a gun in his hand. Jack took out his gun as well, and pointed it towards the man. His appearance was utterly terrifying and disgusting all at the same time.

His eyes seemed to flow a deep, devil-like red. His hair was almost nonexistent, as it was a buzz cut. The hair he did have was gray.

His clothes weren't any better, they were ripped up, but he had a belt on with blood and... _tools_ attached to it.

"How the hell did you get in?!" Jack yelled, his hand with a firm grip on his pistol.

"Destroyed your alarm and lockdown mechanism." The man explained.

"Who are you?" Jack demanded.

"My name is Jet, and I'm here to retrieve my...property." Jet advised, and shot Jack in the chest.

Once Jack was down, Jet rushed down to the medbay and smiled when he saw the Doctor. He shook him awake, violently. The Doctor slowly opened his eyes, and yelled when he saw his former captor's face.

"No, no, no, no, no, please, leave me alone." He curled in on himself, and started panicking. He hyperventilated and caused his respiratory bypass to kick in.

"Oh, I see they've put a cast on your leg. We can't have that now, can we?" Jet smirked.

He detached a hammer with spikes on it from his black vest, and positioned it above where the Doctor's femur would most likely be hurt the most. He hit the Doctor's leg with all the force he was capable of, and the Doctor screamed in agony.

"Perhaps you need to be reminded as to why you deserve this, _Time Lord_." Jet smiled, and put his fingers on each of the Doctor's temples.

He saw his planet burning, the orange sky invisible due to all the smoke. His family was on the ground, dead.

The next horrible thing Jet made him see, was the image of Rose walking away with his duplicate. All the emotions from that day came back. Heartbreak from Rose kissing someone else beside the real him. Sadness from the reminders of all the people who died in _his_ care. Harriet Jones, Peri, Adric, Jabe, River, Lynda, and worst of all, his whole race.

His fingers left the Doctor's temples, and he came back to reality. Self hatred went through his mind. He murdered his own race, and it all turned out to be for nothing. The Daleks still came back.

"Now, you get your last punishment, Doctor." Jet brought the hammer above the Doctor's unbroken leg, and smashed it. Once again, the Doctor screamed. He was about to strike once again, but a gunshot was heard. It was Jack. He had shot Jet. Jet was gone now, he was safe from that monster. But, his leg was screaming. Fuck, it hurt.

Jack ran over to the Doctor's side, and hugged him. Tears were streaming down the Doctor's cheeks, and he was full on sobbing. Jack patted his back and spoke a variety of comforting words. Once the Doctor calmed down, Jack called Martha even though it was three in the morning.

"Get to the Hub, NOW. There's been an attack and the Doctor's hurt." Jack advised, not bothering with a greeting.

"Alright." Martha understood by the urgency in Jack's voice that this was beyond serious. She left a note for Mickey, and headed out to her car.

Jack waited by the Doctor's side, waiting for Martha to arrive.

"Jack, my legs, they hurt so bad." The Doctor struggled to speak without crying out in pain. His legs felt terrible. Not only did he hate himself at the moment, but he was in absolute agonizing pain.

"I know. What's the highest dose of Morphine you can take?" Jack asked, wanting to rid the Time Lord of all pain.

"200 mls." Jack spun the switch on the Doctor's machine that connected the drip to him to the correct number, and within five minutes, the Doctor felt less pain.

"Thank you, Jack." The Doctor genuinely was grateful for his _friend_. Even after he left without Jack on the Gamestation, he still stood by him. He didn't deserve such a great ally. At least, that's what he believed.

"Doc, there's I need to confess. I've been holding it in for so long now, and I need to tell you." Jack was frantic, could he really admit his love at a time like this? Was he brave enough? He really didn't know. He just needed the Doctor to be aware of his feelings.

"Alright." The Doctor nodded.

Jack straightened up and sighed. This was going to have to wait, he decided. He tried to think of a false confession, but his mind was blank. _Thank you for being in my life-No. I absolutely adore y-NO! Fuck, what should I say?_ Jack could not think of anything.


	4. Chapter 4

The Doctor noticed the thoughtful expression on Jack's face, and cleared his throat. This broke Jack out of his thoughts with a gasp.

"Jack, what is it? You can tell me." The Doctor advised, comfortingly.

"Um...It should wait till later." Was the best response he could think of.

"Ja-a-a-ack, now I'm going to be wondering forever!" The Doctor moaned.

Jack chuckled, and took hold of the Doctor's hand. The Doctor smiled, reassuring him that holding his hand was okay. Abruptly, the Doctor winced.

"Blimey, my head hurts." He grabbed his head with both of his hands, groaning.

"Have you had any water, recently?" Jack asked. He hadn't seen the Doctor drink anything within a few hours, so dehydration might have been affecting him.

"Oh no, it's the TARDIS. Something's wrong." The Doctor's eyes clenched shut, he gripped his head tighter, and yelled in pain. The TARDIS needed him.

"Jack, you've got to go check on her." He yelled louder as the pain increased. Jack nodded and ran up to the main area of the hub, noticing Martha walking in. She had heard the Doctor's yelling, even from behind Torchwood's rolling door.

"Jack, what the Hell is going on?" She demanded. She'd just arrived, and it seemed things were going horribly.

"Go take care of the Doctor! I have to get to the TARDIS!" Jack yelled back, and continued venturing to the Time Lord's ship. Once he got inside, he felt that the aura completely changed. Usually when he entered the TARDIS, he'd feel a blast of warm air and a mental comfort. This time though, it felt saddening. It was freezing. Not cold like the Doctor preferred, but completely and totally freezing.

Jack immediately regretted not bringing his favored coat. He ignored the cold as best as he could, and walked closer to the TARDIS console. He swiped his hand along its top, and tried to make a connection.

 _Doctor...Doctor...Come back...I miss you._ Jack heard all of the ship's thoughts, and shuddered. No wonder the Doctor was in so much mental pain.

"Hey beautiful. The Doctor's safe. He's injured, but safe. I promise." Jack felt a blast of warm air, in complete contrast to the freezing cold that was there only a few seconds ago.

Jack smiled, and left the now sated timeship. He walked down the steps back to the medbay. The Doctor was sleeping, and Martha was sitting on a stool next to the unconscious Time Lord. Everything seemed to have had died down, which made Jack feel extreme relief. Hearing the Doctor scream like that always broke his heart.

One Hour Later

Martha came back out from the medbay, and smiled at Jack. He was asleep. He needed it, after all. Martha knew it due to the horrible bags under his eyes. He'd obviously been working very hard to take care of the Doctor. _Typical Jack_.

Martha covered immortal friend with a duvet, careful not the wake him. It was nice that both Jack and the Doctor were resting.

She headed out of the hub, knowing Mickey probably wasn't so fond of her staying at the Hub too long. Even though the Doctor was extremely important, she decided a long time ago she always was going to put family first. After The Year, her family was traumatized. That was why she left the Doctor, after all. Her family needed her.

Jack woke up only half an hour after Martha left, and rubbed the sleep out of his eyes. His mind automatically drifted to the Doctor.

Something wasn't right. Jack looked to where the TARDIS was _supposed_ to be. The TARDIS was gone, and so was the Doctor. Jack practically leapt off the couch, and ran up to his office. There was a note that was almost certainly from his missing Time Lord friend.

 _Thank you, Jack._

It was signed in a different language. _Gallifreyan_ , Jack thought. He was angry, worried, and disappointed. He never told the Doctor the truth about his feelings for him. He was still injured mentally and physically, how could he leave like that? He called Martha after calming down.

"Hello?" Martha had obviously been asleep.

"The Doctor's...Gone." Jack advised

He could hear background noise and a door shut over the phone.

"Where is he? What do you mean, 'gone'?" Martha had urgency in her voice that Jack hadn't heard since Davros had returned.

"He left, Martha. But I think it's okay."

"I-Alright. I'm going to try calling the TARDIS." Martha hung up without Jack being able to reply.

The Doctor stood outside of the TARDIS, in front of Martha's apartment building. He heard the phone ring from the outside, and opened the little door in front of it.

"Are you alright, Doctor? Where've you gone?" Martha stumbled over her words. She was worried.

"I'm okay, really. I healed myself. The TARDIS equipment helped." He told Martha, leaning against the TARDIS' door.

"Will you be okay? You know, alone?"

"Yes. I'll be fine, I promise. I should go. Tell Jack I'm okay." The Doctor hung up.

Martha told Jack everything. Of course he was still angry, but relieved the Doctor was okay.

He would see him again, he was sure.

 **After The 456 and The Miracle**

Jack sat in a bar with different species of all kind around him. He sipped an alien drink, while reminiscing about Gwen, Ianto, Tosh, Owen, and Steven. He killed his own Grandson. But what other choice did he have? He couldn't let the 456 take all of those children. He thought about Esther and how she had to die. He lost everyone, but why him? Why did _he_ have to lose everyone?

He could visit Gwen, but he doubted she wanted to see him after all the shit that his Torchwood caused for her. She lost her closest friends and the best job she'd ever had. Jack had nowhere to go.

A waiter slid a note to him, and said, "It's from the man over there." and pointed towards the last man he thought he'd see on this terrible day. It was the Doctor.

Jack opened the note which said,

 _His name is Alonso._

He looked back at the Doctor, expecting an explanation. The Time Lord simply moved his head, gesturing to a man next to him. He looked like he'd been through Hell, and like a crew member from some type of ship.

Jack looked at the Doctor again, and mindlessly saluted him. Something told him he wouldn't see him ever again, but another told him it would just be a while.

Either way, he would wait as long as he needed. He would see the Doctor again, and he would tell him what he was never able to.

 **This was definitely one of the most stressful stories I've ever written. It took a lot of effort to finally finish it, and I'm not exactly happy with how it turned out. Thanks to all who have followed this story and waited for me to update. You're awesome!**


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